Table 5 The running time and SP score of single core HAlign and CMSA(CPU) based on different center sequence selection algorithms
From: CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment
Dataset | Num | Center sequence | Running time(s) | Average SP score | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HAlign | CMSA | HAlign | CMSA | HAlign | CMSA | ||||||||
Step1 | Step2 | Step3 | Overall | Step1 | Step2 | Step3 | Overall | ||||||
MT | 672 | 16 | 479 | 88.19 | 33.40 | 21.11 | 142.70 | 0.80 | 43.40 | 0.50 | 44.70 | 0.977 | 0.987 |
1000 | 912 | 575 | 2.22 | 0.42 | 0.24 | 2.88 | 0.05 | 0.40 | 0.03 | 0.48 | 0.549 | 0.570 | |
D1 | 3000 | 912 | 575 | 23.17 | 2.75 | 0.77 | 26.69 | 0.13 | 1.20 | 0.10 | 1.43 | 0.550 | 0.588 |
5000 | 3477 | 2266 | 67.95 | 2.10 | 1.28 | 71.33 | 0.16 | 2.15 | 0.23 | 2.54 | 0.492 | 0.523 | |
1000 | 158 | 158 | 6.93 | 0.52 | 0.99 | 8.44 | 0.07 | 1.40 | 0.10 | 1.57 | 0.508 | 0.548 | |
D2 | 3000 | 181 | 1447 | 70.64 | 5.07 | 1.20 | 76.91 | 0.18 | 4.90 | 0.25 | 5.33 | 0.484 | 0.500 |
5000 | 3533 | 4677 | 200.38 | 10.31 | 7.60 | 218.29 | 0.25 | 0.96 | 0.42 | 1.63 | 0.455 | 0.510 | |
1000 | 697 | 697 | 13.50 | 2.19 | 1.85 | 17.54s | 0.12 | 4.22 | 0.17 | 4.15 | 0.513 | 0.540 | |
D3 | 3000 | 2170 | 3217 | 125.06 | 2.19 | 1.85 | 129.10 | 0.24 | 13.44 | 0.34 | 14.02 | 0.527 | 0.528 |
5000 | 2420 | 2992 | 351.49 | 8.40 | 9.75 | 369.64 | 0.37 | 22.13 | 0.60 | 23.10 | 0.518 | 0.523 | |